Im hooking up a project on my motorcycle- using a Arduino micro which doesn't have a barrel jack and I'd prefer to not use the Vin/Grnd because I already have a usb hub hooked up on my bike (for charging other devices)

My concern though is- does the USB input have any voltage protection? I tested the voltage on my usb hub and i see it hover between 5 and 6 volts... is that okay or could this damage my Arduino?

6V is the Absolute Max begore damage is likely to occur. 12V is right out!You can take the 6V and run it thru a couple of 1n4001 type diodes to drop it down to ~5.3, 4.6 kind of range and then bring power in via the USB connector.

At 12V the small voltage regulator has to dissipate the 12-5 = 7V. It might get hot.If you can't keep your finger on the voltage regulator, it is too hot.Can you try using 5V at Vin and measuring the +5V output pin of the Arduino ? I don't have a Micro myself to test it.